Nucleic acid reactions, catalysis

Nucleic Acid-Based Catalysis Reaction Geometry and Effective Concentration... 

Hydroxyl radicals OH, which attack proteins, nucleic acids, and a large variety of other cellular constituents, may also be formed. Although too reactive to diffuse far, they can be generated from H202 by Eq. 18-68. This reaction involves catalysis by Fe ions as shown.5623... 

Biological Reactions. Biosynthesis and catabolism of biological molecules (amino acids, carbohydrates, lipids, nucleic acids, peptides/proteins), metabolic cycles, biological catalysis and kinetics, mechanisms, organic and inorganic cofactors. 

Figure 1. Catalysis and template action of RNA and proteins. Catalytic action of one RNA molecule on another one is shown in the simplest case, the "hammerhead ribozyme." The substrate is a tridecanucleotide forming two double-helical stacks together with the ribozyme (n = 34) in the confolded complex. Tertiary interactions determine the detailed structure of the hammerhead ribozyme complex and are important for the enzymatic reaction cleaving one of the two linkages between the two stacks. Substrate specificity of ribozyme catalysis is caused by secondary structure in the cofolded complex between substrate and catalyst. Autocatalytic replication of oligonucleotide and nucleic acid is based on G = C and A = U complementarity in the hydrogen bonded complexes of nucleotides forming a Watson-Crick type double helix. Gunter von Kiedrowski s experi-...

The rotaxane assembly is adopted by many enzymes that operate on nucleic acids and proteins. In the case of processive enzymes, the catalytic reaction drives the sequential motion of the enzyme on its polymeric substrate. Therefore, these enzymes can be viewed as molecular motors powered by chemical reactions and moving one-dimensionally on a track, in which fuel is provided by the track itself. An initial attempt to carry out processive catalysis with a synthetic rotaxane has been described [69]. 

The demonstration that the polymerase chain reaction can be carried out in liposomes [50] is important because it demonstrates that liposomes can resist the required temperature changes. In the light of the lipid world model it is useful to ask what catalytic functions Luisi s structures show behind direct auto catalysis. Binding of peptides to and polymerisation of amino acids in liposomes was demonstrated in various systems [51]. We are not aware of a similar effect on nucleic acid synthesis. 

Hydrolytic catalysis by metal ions is also important in the hydrolysis of nucleic acids, especially RNA (36). Molecules of RNA that catalyze hydrolytic reactions, termed ribozymes, require divalent metal ions to effect hydrolysis efficiently. Thus, all ribozymes are metalloenzymes (6). There is speculation that ribozymes may have been the first enzymes to evolve (37), so the very first enzymes may have been metalloenzymes Recently, substitution of sulfur for the 3 -oxygen atom in a substrate of the tetrahymena ribozyme has been shown to give a 1000-fold reduction in rate of hydrolysis with Mg2+ but no attenuation of the hydrolysis rate with Mn2+ and Zn2+ (38). Because Mn2+ and Zn2+ have stronger affinities for sulfur than Mg2+ has, this feature provides strong evidence for a true catalytic role of the divalent cation in the hydrolytic mechanism, involving coordination of the metal to the 3 -oxygen atom. Other examples of metal-ion catalyzed hydrolysis of RNA involve lanthanide complexes, which are discussed in this volume. 

However, not all cleavage reactions of nucleic acids promoted by metal ions occur through direct involvement of metal ions in cleavage chemistry. For example, metal ion cofactors stabihze the catalytically active conformations of several ribozymes, but do not participate directly in catalysis. ... 

Enzymes are proteins that catalyze biochemical reactions. A catalyst is a substance that greatly accelerates the rate of a particular reaction without being used up or permanently altered- In the real world, most catalysts eventually deteriorate and no longer function as a catalyst. In the cell, all enzymes are eventually degraded and converted back to their constituent amino acids plus, in some cases, byproducts of oxidation or other types of damage- Ptoteins do not have some unique magical property that allows them to function as enzymes. For certain activities nucleic acids also participate in the chemistry of catalysis- For example, mRNAcan catalyze certain types of RNA splicing. 

Tempcrature-jump methods have not been used in soil science. However, they have been widely employed in many areas of chemistry and biochemistry research to study the following types of reactions (Turner, 1986) electron transfer, enzyme catalysis, metal complex formation, nucleic acid folding, proton transfer, spin equilibria, and protein-ligand binding. 

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